[choreo] General cleanup and improvement of backend

[oh-yes-0-fps]

I kinda goofed and got carried away :3

• Expanded the capabilities of the upgrader and add better documentation for it.
• Cleaned up the generation code and by doing that fixed the bug that caused the cli to override the waypoints rotation.
• Removed the integration test from where it is now and will add it into the cli crate b4 merging this to prevent silly code duplication.
• Removed the writer indirection for trajectories and projects, i don't remember why it was even a thing to begin with